hello bisque 130 this is the beginning of recorded lecture one two uh getting started on chapter 2 The Chemical foundation of life so kind of like that first chapter this is another groundwork chapter uh I expect that if you've taken any chemistry class in high school or if you're taking a chemistry class at Tech uh that you know you know all this stuff already but there are technically no prerequisites for you know my class bisque 130 so we got to go through all this just to to get everyone on sort of a baseline of understanding so um a lot of key terms in this chapter just like the last one but yeah that's what these foundational chapters are kind of like so let's start with some real simple stuff and Define matter so yeah straight off the bat key terms uh matter is reading from the key terms now anything that has mass and occupies space so yep that includes atoms and uh yeah all the stuff smaller than atoms which we'll talk talk about soon yeah all the all these things are matter um another important term here is elements so yeah I referenced the mentioned the periodic table last time yep do not memorize this in any way but uh yeah these are all different flavors uh of atoms that we call Elements uh elements are just different types of atoms uh I can read the definition of elements um the key terms definition of element is one of 118 unique substances each element has unique properties and a specified number of protons protons soon enough uh but you know elements just different types of atoms and you could diagram all these in the periodic table which the key term just says is an organizational table showing um these different elements and their numbers and key information about them so let's talk more about these these building blocks of atoms these more the components of an atom so there are three important components to any atom protons in this diagram in blue neutrons in this diagram in red and electrons in this diagram in green there are several different ways to draw an atom this kind of diagram uh that shows the electron sort of whizzing around uh this Central Area the central nucleus of the atom is probably the most accurate way to draw what this looks like uh however if we're counting protons and electrons and stuff like that and and trying to to see things clearly this is less accurate but this is probably the most common way of drawing an atom where you can clearly see the protons neutrons and then be able to count those electrons so let's start by talking about protons uh well we can see here there's a big old plus sign on these blue protons here they are positively electrically charged and they reside in this center part of the atom called the nucleus or Atomic nucleus let's run down some of these stats positively charged in the atomic nucleus mass of one so AMU is atomic mass units it's just a unit for describing the mass of really really really really really really really small things you know like the components of an atom protons they got a mass of one so you know these are their properties but what does the proton actually do well the protons Define how an atom behaves uh hydrogen is hydrogen and does hydrogen things because it has one proton that's the number in the corner up here uh if it had seven protons it wouldn't be hydrogen anymore it would be nitrogen and it would behave like nitrogen and would do all the nitrogen things so yeah the the number of protons is incredible ibly important it defines which element a given atom is number of protons defines an atoms Elemental properties and its atomic number that's the you know number you see in the top left hand corner in a periodic table so very important another component here I want to talk about continuing on with the the nucleus are the the neutrons so you know it's right there in the name n uh these are not positive these are not negative neutrons have a neutral charge uh they are also in the atomic nucleus right next to those protons and you can't see it from looking at it but they also have a mass of one so neutrons neutral charge in the atomic nucleus mass of one AMU so they've got one just like protons have one so the neutrons don't impact what the element is you know you could be carbon with a certain number of neutrons you add or remove neutrons and it's still going to be carbon it's carbon because of the number of protons but you can have different numbers of neutrons it's not going to affect the elemental properties but it's going to cause something called Isotopes so here is carbon 12 it's got six protons six neutrons um 6 plus 6 is 12 see why it's called carbon 12 um and here's what we call carbon 13 it's got six protons and neutrons remember neutrons have an atomic mass of one so adding an extra Neutron is going to increase the mass by one this is carbon 13 because 6 + 7 equal 13 and then there's carbon 14 with eight neutrons 6 + 8 equals 14 all of these things are still carbon you could still use them like carbon they behave like carbon but they do have slightly different properties uh again we don't call these different elements they're all car carbon uh we call these things with varying numbers of neutrons we call these things Isotopes so atoms of the same element can have different numbers of neutrons we call these things Isotopes so neutrons don't affect the element they affect the the isotope of that element okay we got one more here we know it's coming it is the electrons these are different in a couple of ways so yeah these have a negative electrical charge they are not in the Aton IC nucleus they orbit around the outside and again it's it's more accurate like this they don't actually you know orbit like planets around a star but it's very convenient to draw them like this and they have a mass of well it it's not one um I I I will annoy the physicists if I say it's zero because it's technically not zero but the mass of an electron is so incredibly tiny compared to the mass of proton and neutrons we can basically ignore it I mean go back to this it was carbon 12 because it had six protons six neutrons it didn't matter how many electrons were in here probably six uh you know because they just don't impact the mass at all the phrase that I like is that they lack functional Mass again it's not zero but it's so small we don't care about it in biology at least so electrons um also known as e super script minus so this is a very common shorthand not just for taking fast notes but you will see throughout the quarter in a lot of uh figures and diagrams the little e superscript minus sign that means electron so electrons yes they've got a negative electrical charge they orbit around the atomic nucleus and yeah this this phrase they lack functional Mass so that does mean um if you're wanting to count these things up the mass of an at equals the number of protons it has plus the number of neutrons it has number of electrons don't really matter when it comes to this uh and we saw this with carbon just another kind of note here most elements have the same number of electrons as protons we saw this in carbon um I guess it's hard to count the protons here because they're kind of overlapping one another but we know carbon based on the periodic table of the elements boom know these numbers are kind of small to see there's a six here carbon has six protons and let's count them one two three four five six six electrons I'm you know calling out the electrons and protons because these are the ones that contribute to the charge there are exceptions but many of the elements we are going to come across are going to have the same number of electrons as protons the same amount of negative charge and positive charge so they're going to cancel out and this is this is not a charged atom so most elements in biology um have the same number of electrons as protons giving them an overall neutral charge again there are exceptions to this in the periodic table but yeah this is generally what we see in a lot of stuff that we care about in biology now if you take a chemistry class you will understand why the following statement is true but in an introductory biology class I don't want to get bogged out in the details here I'm just going to make this statement and trust me there's a reason behind this but trust me that this is true atoms are most stable when they have specific numbers of total electrons those magic numbers that we care about not magic but you know these special numbers these particular numbers that we care about uh in biology are 210 and 18 total electrons so like I just said most elements have the same number of electrons as protons so if we go back to this table here uh yeah helium two protons and two electrons it's stable it's good uh neon 10 protons because it's atomic number 10 10 electrons it's stable uh there's argon with 18 and so on yeah these things are fine but most other things are not most other elements here don't have by default 2 10 or 18 total electrons which means they're not as stable as they could be so because these atoms are not as stable as they could be they're going to do whatever they can to get to these total numbers they're going to form chemical bonds with one another in order to achieve this stability so this is the the reason why chemical bonds are made to get to these stable numbers so the key terms define a chemical bond as an interaction between two or more of the same or different atoms that results in the formation of molecules so yeah I mentioned molecules in the last chapter uh these are things that hold molecules together so there are several types of chemical bonds we'll talk about three starting with something called calent bonds these are probably the most common type of chemical bond that we're going to see in biology a calent bond to again just read from the key terms is a type of chemical bond semicolon forms when electrons are shared between atoms so let's take a look at this here is a calent bond between two hydrogen atoms so a little bit of background hydrogen by default has one proton uh most of them have have zero neutrons and one electron so one is not one of those happy numbers of 210 or 18 so this default hydrogen is is really looking to get a second electron here's a hydrogen here's another hydrogen and look what they've done they've shared their electrons with one another so there're again this is one way of drawing this really these two electrons are going to be sort of you know moving back and forth between these two atoms and a cloud of probability around them uh but yeah each one of these contributes uh to each of these so this hydrogen has one two electrons it is stable this hydrogen has one two electrons it is also stable these two electrons are being shared between the two uh you will see this written as a single Dash a single line between the two elements when you're writing out or or seeing written out um chemical compound structures H line h indicating that there's a single calent Bond here now this confuses a lot of students it is called a single calent Bond even though there are two electrons being shared because as we're going to see electrons are shared in pairs so this is a single pair of electrons uh that's why it's called a single calent Bond and again this is very strong this is a this is a close relationship between these two atoms it's pretty difficult to break up these two hes uh but again it doesn't always have to be one pair sometimes it can be two here's oxygen it's got 1 2 3 4 5 6 78 I guess we can go back to the periodic table there's oxygen atomic number eight again I don't expect don't don't memorize any of this don't don't memorize you know how many protons boron has or or you any of this stuff I'm going back to reference this but by no means should you memorize anything on this periodic table uh but here's an oxygen it's got eight total electrons that is not one of those stable numbers it is pretty close to 10 though it needs two more electrons to get there and it can get there by sharing not one pair but two pairs of electrons with another oxygen for example so now this oxygen has 1 2 3 4 5 6 7 8 9 10 it's happy this one has 1 2 3 four 5 6 7 8 nine 10 it is also happy and again there are two pairs being shared here so this is a double calent bond and you'll see it drawn like this the two lines uh between the two atoms now there is a triple bond that can occur which obviously shares three pairs with nitrogen here 1 2 3 4 5 6 7 8 9 10 you know each one of these are stable this is not very common in biological molecules but I do want to call it out as existing uh three lines here between the two atoms uh yeah the triple bonds do exist so these are uh all types of calent bonds which yeah I had earlier this is very strong a calent bond is a very is the strongest type of chemical bond that we're going to talk about uh electrons are shared in pairs one pair single calent Bond two pairs double calent bond three pairs triple calent bond and I do want to point out all of these examples were the same element like hydrogen sharing with hydrogen oxygen sharing with oxygen nitrogen sharing with nitrogen it doesn't have to be that way they don't have to be the same element here's an example of oxygen sharing electrons with hydrogen so yeah there is a single calent Bond here between the oxygen and the hydrogen um and this illustrates another thing it doesn't always have to be just a single bond between two atoms sometimes atoms can have multiple partners multiple bonds to different atoms so yeah here's this oxygen forming a single coal bond with this hydrogen and then another single calent Bond uh with this hydrogen here so this is of course H2O this is of course water uh but yeah this is this is just another example of this two separate single covalent bonds this one atom a bond to this atom bond to this atom and they're different elements so just more examples of this now there's another thing that can happen in in the the Quest for for stability trying to get to 2 10 or 18 total electrons some atoms can achieve this stability by permanently gaining or losing an electron or two so before I read the rest of the slide let's see an example of this so here is sodium by default sodium has 1 2 3 4 5 6 7 8 9 10 11 electrons and 11 protons 11 it's so close to 10 it would have to have uh you know seven more Partners if it wanted to get to 18 but it it's it's much closer to 10 the easiest way for sodium to get to its 10 stable electrons would be to just lose this 11th electron uh so it gives away this 11th electron it gets 10 total electrons it's more stable this way but now it's not balanced now it has 10 electrons but it has 11 protons here in the nucleus there's one more proton than electron which is going to give it A+ one positive charge here's another example of sort of the opposite situation here's chlorine by default it has 1 2 3 4 5 6 7 8 9 10 11 12 1 14 15 16 17 total electrons and 17 protons that is very close to 18 and yes it could try to F form a single calent bond with something like hydrogen to get to 18 but in such a big bulky element it's much easier for it to just get that 18th electron permanently so this results in what is called a chloride ion it's got 18 electrons but again it's unbalanced now it has one more electron than proton so it has a negative charge remember electrons are negatively charged so this is not a bond I'm working towards that uh but so far this is just backstory to our second chemical bond some elements some some atoms permanently gaining or permanently losing an electron or sometimes two um when this happens they become an ion which we we saw that but let me read the key terms definition here an ion is an atom or chemical group that does not contain equal number of protons and electrons so yeah something that's charged an ion is something that's charged and it comes in two flavors anion and catons um one of these is positive one of these is negative which one is which uh well to me my dumb way of remembering which one is which you see a little lowercase T here in cat that lowercase T looks a lot like a plus sign to me and if you remember that little visual clue that'll tell you which one is which an an ion is reading from the key terms a negative ion that's formed by an atom gaining one or more electrons and a cat is a positive ion that is formed by an atom losing one or more electrons so yeah just some back uh some terminology here anion or cations so where's the chemical bond well it is a fundament force of the universe that positively charged things and negatively charged things are attracted to one another so if you have cations and anion together they will form what is called an ionic bond notice there's no sharing of electrons here this is just the attraction between a positive atom and a negative atom this is an ionic bond holding together sodium cation chloride anion forming good old sodium chloride or or table salt so this is the bond the ionic bond key terms a type of chemical bond that forms between ions with opposite charges and they're not sharing it's just this attraction between positive and negative and I'm not going to put any numbers to how strong these things are but but it is worth pointing out that ionic bonds are weaker than Cove valent bonds again Cove valent bonds the sharing it's the strongest thing that we'll talk about now our third type of of chemical bond is a little complicated we need a little backstory to talk about this third one so a lot of text on this slide sorry some elements are some elements don't play nice so you know before we look at this text here some elements will share electrons but they will not share evenly oxygen is one of these elements so yeah here is O we saw this a few slides ago in in water uh here's oxygen here's hydrogen here is a single calent bond between the two there are going to be two electrons that are being shared between these two atoms but oxygen is an electron hog it's greedy with its electrons the technical term is it's electr negative so even though there are two electrons being shared they're not being shared equally the oxygen is spending more time with these electrons remember electrons are negatively charged so if this atom is spending a disproportionate amount of time with negatively charged electrons that's going to give it a negative charge not a full negative charge it's not permanently gaining anything there's still being shared it is a partial negative charge that's what the lowercase Delta means uh it has a partial negative charge in contrast the hydrogen is not getting an equal you know its fair share of time with these negatively charged electrons it is going to take on a partial positive charge so let me summarize this some elements are more electr negative than others again that's the technical term for being electron greedy oxygen is a a very good example of this in Cove valent bonds um these electr negative elements share electrons unequally this results in what is called a polar Cove valent Bond so yeah this is kind of going back to calent bonds this is a type of Cove valent Bond when they're not being shared equally we call it polar uh this creates partial charges in both of those atoms and yep in an O doesn't matter whether this o is part of water or part of any other molecule if you've got an oh as part of any sort of chemical compound you're going to have this unequal electron sharing the O is going to become partially negatively charged and the hydrogen is going to become partially positively charged now one other kind of side note here um it is possible for electrons to be shared unequally it is also possible for electrons to be shared equally so carbon is an example of an element that does play nice here's carbon and hydrogen together and yeah there's no charge here there's no partial negative there's no partial positive they're being shared pretty equally between between the two so I just wanted to point out the uh the terminology here when electrons are shared equally this is called a nonpolar Cove valent Bond and there's no charge or any of this stuff involved CH classic fantastic commonly occurring example of this no charges of the carbon or hydrogen when you got CH uh partnered up together so okay this is all this was all backstory because this is not a new type of bond these are just you know different types of Cove valent bonds there's a new Bond here that we call hydrogen bonds hydrogen bonds are attractions between the partial negatives and the partial positives in two different molecules or groups so again fundamental force of the universe positive is attracted to negative that's true when we had full charges that is still going to be true when we're dealing with these partial charges here's a partially positively charged hydrogen it's partially positively charged because the oxygen it's it's partnered with is is hog and the electrons this partial positive is attracted to this partial negative uh in the water over here this right here is the hydrogen bond and I I like this figure as well it doesn't show the the O's and the H's quite so clearly but this is showing that yeah this right here between this oxygen and this hydrogen this is a calent bond this is a Cove valent bond this is a Cove valent bond this is a calent bond calent bonds hold these molecules together the hydrogen bond is the interaction between these two separate molecules hydrogen of this H2O oxygen of this H2O there's the hydrogen Bond there's the hydrogen bond as you could probably guess this is the weakest of the three it's definitely weaker than an ionic bond this is a full positive and full negative uh obviously partial positive partial negative is going to be weaker uh so hydrogen bonds there is a key terms definition I think we did a good job of of walking through this but if you want a summary of this the key terms define a hydrogen bond as a type of chemically chemical bond between slightly positively charged hydrogen atoms and slightly negatively charged atoms in other molecules so the positive always has to be a hydrogen it's why it's called a hydrogen bond the negative thing is just whatever just anything else that's negative usually it's an oxygen but just anything else that's negative that makes it a hydrogen bond um common abbreviation is to call them H bonds hydrogen is H in the period iodic table so H bonds hydrogen bonds same thing and yes this is the weakest of the three this is weaker than ionic bonds we had coal strongest ionic in the middle and hydrogen bonds as the weakest of the three even though these are very weak we are going to see in certain macro molecules thousands and millions of hydrogen bonds holding these things together they're weak but when there's a lot of them they could do very impressive things so in sort of grand summary here uh all of these chemical bonds are important in holding together all of this stuff organic molecules macro molecules organel and cells all these big structures are held together by these chemical bonds we've we've just talked about oh and you know I think I've been throwing out this term organic molecules this is the first time I've highlighted it in the key terms if you're curious an organic molecule is defined as any molecule containing carbon except carbon dioxide so we will see organic molecules um in you know this chapter and the and the next chapter you know things like sugars are organic molecules proteins are organic molecules if you see their structures anything with carbon except CO2 uh is defined as an organic molecule so just keep that definition uh in mind here all right let's finish up this recorded lecture by talking about water so water is very important for life for a lot of different reasons so water has partial charges both negative and positive and we saw this in this figure here any given H2O you know the oxygens are all partial negative the hydrogens are all partial positive so if you're talking about you know a cup of water or puddle of water or whatever it is that whole thing has a bunch of positive charges and a bunch of negative charges this means water is really great at interacting with anything else that is charged um take a look at this so uh we all know that salt dissolves in water and here's why so here's the negatively charged chloride ion yes it was happily ionically bonded with the the sodium um full positive charge but when it's in water it gets to be fully surrounded in three dimensions by the way we're looking at a flat image here but in three dimensions this chloride ion gets to be surrounded by the partial positive charge hydrogen and sodium gets a similar treatment surrounded by the partial negatively charged oxygen here's something else we know dissolves in water sugar dissolves in water and here's why look at this sugar molecule don't memorize this but look at all these O's remember what happens every time you've got an oh whether it's part of water or anything else anytime there is an O maybe I should show this anytime there's an O the O is going to be partial negative the H is going to be partial positive well if sugar is in water all those partial positive H's get to be with partial negative O's on molecules of H2O H2O H2O just fully surrounded in three dimensions this is why water is great at dissolving in stuff anything charged whether it's partially charged like this sugar fully charged like this salt it's going to love being in water because it gets to be surrounded by its opposite charges so in summary because of those partial charges in water it interacts with it dissolves anything else that is charged so there's a term for this we call these things that that love being in water uh we call these things hydrophilic so anything that's charged we call hydrophilic hydrophilic atoms and molecules will dissolve in water sodium chloride glucose great examples of this in contrast if something is not charged it doesn't want anything to do with water we call these things hydrophobic uh yeah uh felos means love phobia means fear obviously Hydro means water so yeah hydrophilic means water loving hydrophobic means water fearing uh yeah atoms and molecules um that are hydrophobic do not dissolve in water and yeah oil great example of this pour some oil on top of some water it's not going to dissolve it's going to Clump together with itself if we look at the chemical structure of fats and oil which we will in later chapters uh you'll see that they're not charged at all so yeah they don't want anything to do with water we call these things hydrophobic now there's a reason why when astronomers uh going far a field for this this explanation here but there's a reason why astronomers look for water on other planets and moons when they're looking for Life water has so many properties that are convenient for life that it's hard to imagine life existing and being sustainable in the absence of H2O in the absence of water so just listing out here some of these properties of water that are convenient for life one of these water is a very effective solvent so what is a solvent well we've already we've already seen a solvent in Action a solvent is just something that dissolves things if I can read from the key terms here a solvent is a substance capable of dissolving another substance and again because of all these charges water is fantastic at this and again just for a perspective we're comparing water to other liquids that you would find on other planets and moons and and things like that compared to liquid ammonia or ethanol or acetone or you know other stuff like that water is great at dissolving things fantastic solvent another property of water that's very nice is that water is sticky and again we don't normally think of water being sticky we think of you know honey or syrup as being sticky but again if you're comparing H2O to ethanol acetone you know liquid methane liquid ammonia whatever it is very sticky water absolutely sticks to itself we see this phenomenon with uh you know raindrops drops of water uh this will not happen with ethanol uh it's so sticky uh and we know exactly why it's sticky as well water loves to stick to itself because every single H2O is going to be hydrogen bonding with all the other h2os that it can find surrounding it water loves it self water loves to stick to itself we call this property cohesion the key terms define cohesion as oh I'm sorry cohesion is uh actually not in uh the key terms uh cohesion just means that it sticks to itself um it's my mistake here um surface tension however is in the key terms uh surface tension is what happens when water would rather stick to itself than break so because water loves sticking to itself so much you can actually apply some amount of force to this water and not break the surface of this it would rather stick to itself surface tension um reading from the key terms here again sorry about this dynamically changing no no cohesion um it's just water sticking to itself surface tension is tension at the surface of a body of liquid that prevents the molecules from separating so yeah very convenient for you know C C organisms so water sticks to itself water also sticks to other things so that is what we call adhesion again my bad not in the key terms adhesion is just water sticking to other things and this results in capillary action so we can see water sticking to other things if we shove a narrow tube in a beaker of water and because water loves to stick to other stuff just like it loves to stick to itself this water will fighting against the force of gravity climb up the wall of this tube and this seems like a fun science experiment that doesn't really seem relevant to life uh actually this so-called capillary action of water climbing up the walls of a thin tube because it wants to stick to the walls of that tube is incredibly important for plants this is uh a very important uh aspect effect in how plants transport water from their Roots all the way up to their leaves so again adhesion is just water sticking to other things capillary action reading from the key terms this is something that occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes drawing the water molecules to the sides of the tubes so again very important for plants now there's another important property of water and that is the fact that water ionizes so we know what an ion is we defined that earlier it's something with a a full positive charge full negative charge and th this is something that water just does on its own you got H2O water it can break apart into oh minus and H+ so if you're sipping on a glass of water most of that is H2O but within that water within any cup or puddle or whatever of water there's going to be some amount of oh minus which is called a hydroxide ion negatively charged and there is going to be some amount of H+ in there as well a hydrogen ion also known as a proton so if I can zip back way far back to the beginning of of uh near the beginning of this chapter but by default most hydrogens don't have any neutrons they just have a proton uh one proton and one electron so as it turns out if you take away that electron uh it's just one proton so yeah H+ this hydrogen ion is also just a proton with zero neutrons and it's it's lost its electron so yeah water ionizes it does this thing it breaks apart into the these two ions this is incredibly convenient and important for life because we use these ions a lot we'll see this throughout the quarter especially this H+ the fact that there's just some of this floating around in the cell in the environment is going to be very important we're going to see a lot of chemical reactions that make use of these and this is convenient because water just makes these there's always going to be some of these around in water um I'm just going to say in summary these ions hydroxide and hydrogen are used in many chemical reactions in the cell okay so there's a little bit more about water to talk about but this is typically where I run out of time on things in person so we'll finish up this chapter uh in the next recording this is the end of recorded lecture one two